The integration issues will clearly be very different if the engineering/programming teams will be co-mingled and working on the same product. If they will be combined to work on a single unified product then you are right there will be significant integration costs.

On the other hand if you are buying a company with a product that will continue and the "integration" is at a higher level of abstraction the integration might not be so bad. Support each product on their own stack and integrate at the API level.